Well with Skyrim’s Hearthfire DLC not even a week old seems that Kotaku has reported a major bug that may lock you out of parts of your house.
Luckily you can avoid the bug.
The bug kicks in whenever you try to start work on two projects in the same wing simultaneously. The game seems unable to handle more than one task at a time during home construction. At best, you'll lose progress and at worst the bug will make it impossible to enter certain rooms.
So just complete your rooms and projects one at a time and you shouldn’t have to worry about the bug, at least till Bethesda can fix it in an update.